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Manganese in PDB 1ofq: Crystal Structure of the Tyrosine-Regulated 3-Deoxy-D-Arabino- Heptulosonate-7-Phosphate Synthase From Saccharomyces Cerevisiae in Complex with Manganese(II)

Enzymatic activity of Crystal Structure of the Tyrosine-Regulated 3-Deoxy-D-Arabino- Heptulosonate-7-Phosphate Synthase From Saccharomyces Cerevisiae in Complex with Manganese(II)

All present enzymatic activity of Crystal Structure of the Tyrosine-Regulated 3-Deoxy-D-Arabino- Heptulosonate-7-Phosphate Synthase From Saccharomyces Cerevisiae in Complex with Manganese(II):
4.1.2.15;

Protein crystallography data

The structure of Crystal Structure of the Tyrosine-Regulated 3-Deoxy-D-Arabino- Heptulosonate-7-Phosphate Synthase From Saccharomyces Cerevisiae in Complex with Manganese(II), PDB code: 1ofq was solved by V.Koenig, A.Pfeil, G.Heinrich, G.H.Braus, T.R.Schneider, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.98 / 2.70
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 105.731, 105.731, 268.782, 90.00, 90.00, 120.00
R / Rfree (%) 22.1 / 24.5

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of the Tyrosine-Regulated 3-Deoxy-D-Arabino- Heptulosonate-7-Phosphate Synthase From Saccharomyces Cerevisiae in Complex with Manganese(II) (pdb code 1ofq). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Crystal Structure of the Tyrosine-Regulated 3-Deoxy-D-Arabino- Heptulosonate-7-Phosphate Synthase From Saccharomyces Cerevisiae in Complex with Manganese(II), PDB code: 1ofq:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 1ofq

Go back to Manganese Binding Sites List in 1ofq
Manganese binding site 1 out of 4 in the Crystal Structure of the Tyrosine-Regulated 3-Deoxy-D-Arabino- Heptulosonate-7-Phosphate Synthase From Saccharomyces Cerevisiae in Complex with Manganese(II)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of the Tyrosine-Regulated 3-Deoxy-D-Arabino- Heptulosonate-7-Phosphate Synthase From Saccharomyces Cerevisiae in Complex with Manganese(II) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn1000

b:38.3
occ:1.00
 OD2 A:ASP1342 1.9 39.8 1.0
OE2 A:GLU1316 2.1 39.1 1.0
NE2 A:HIS1282 2.3 38.4 1.0
SG A:CYS1076 2.3 38.6 1.0
CD A:GLU1316 2.9 38.1 1.0
CG A:ASP1342 2.9 40.7 1.0
OE1 A:GLU1316 3.1 35.2 1.0
CD2 A:HIS1282 3.2 37.5 1.0
CE1 A:HIS1282 3.2 38.3 1.0
CB A:ASP1342 3.3 39.4 1.0
CB A:CYS1076 3.4 37.5 1.0
NH2 A:ARG1107 3.9 44.9 1.0
CA A:CYS1076 4.0 37.0 1.0
OD1 A:ASP1342 4.1 40.8 1.0
O A:HOH2011 4.1 49.5 1.0
CD A:LYS1112 4.1 60.9 1.0
CG A:HIS1282 4.3 39.6 1.0
ND1 A:HIS1282 4.3 39.1 1.0
CG A:GLU1316 4.3 36.7 1.0
CE A:LYS1112 4.4 60.8 1.0
NZ A:LYS1112 4.5 59.9 1.0
CA A:ASP1342 4.6 38.4 1.0
O A:CYS1076 4.6 38.4 1.0
N A:ASP1342 4.7 37.7 1.0
C A:CYS1076 4.7 36.7 1.0
O A:HOH2022 4.9 48.0 1.0
CZ A:ARG1107 4.9 43.5 1.0

Manganese binding site 2 out of 4 in 1ofq

Go back to Manganese Binding Sites List in 1ofq
Manganese binding site 2 out of 4 in the Crystal Structure of the Tyrosine-Regulated 3-Deoxy-D-Arabino- Heptulosonate-7-Phosphate Synthase From Saccharomyces Cerevisiae in Complex with Manganese(II)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of the Tyrosine-Regulated 3-Deoxy-D-Arabino- Heptulosonate-7-Phosphate Synthase From Saccharomyces Cerevisiae in Complex with Manganese(II) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn2000

b:52.5
occ:1.00
 OE2 B:GLU2316 2.1 44.5 1.0
OD2 B:ASP2342 2.2 50.3 1.0
NE2 B:HIS2282 2.3 38.5 1.0
SG B:CYS2076 2.6 46.1 1.0
CD B:GLU2316 3.1 45.4 1.0
CE1 B:HIS2282 3.2 38.3 1.0
CD2 B:HIS2282 3.2 38.6 1.0
CG B:ASP2342 3.2 49.9 1.0
OE1 B:GLU2316 3.4 46.1 1.0
CB B:ASP2342 3.6 50.0 1.0
CB B:CYS2076 3.8 43.3 1.0
CA B:CYS2076 4.2 43.3 1.0
NH2 B:ARG2107 4.2 36.6 1.0
O B:HOH3032 4.2 51.4 1.0
ND1 B:HIS2282 4.3 38.5 1.0
OD1 B:ASP2342 4.3 49.8 1.0
CG B:HIS2282 4.4 39.7 1.0
CG B:GLU2316 4.4 44.2 1.0
O B:HOH3046 4.6 41.2 1.0
O B:CYS2076 4.7 44.2 1.0
C B:CYS2076 4.8 43.2 1.0
CD B:PRO2113 4.9 93.0 1.0
CA B:ASP2342 4.9 50.1 1.0
N B:ASP2342 5.0 49.7 1.0

Manganese binding site 3 out of 4 in 1ofq

Go back to Manganese Binding Sites List in 1ofq
Manganese binding site 3 out of 4 in the Crystal Structure of the Tyrosine-Regulated 3-Deoxy-D-Arabino- Heptulosonate-7-Phosphate Synthase From Saccharomyces Cerevisiae in Complex with Manganese(II)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of the Tyrosine-Regulated 3-Deoxy-D-Arabino- Heptulosonate-7-Phosphate Synthase From Saccharomyces Cerevisiae in Complex with Manganese(II) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn3000

b:39.2
occ:1.00
 OD2 C:ASP3342 2.0 39.3 1.0
OE2 C:GLU3316 2.0 40.1 1.0
NE2 C:HIS3282 2.2 37.1 1.0
SG C:CYS3076 2.4 38.5 1.0
CD C:GLU3316 2.9 39.7 1.0
CG C:ASP3342 3.0 40.3 1.0
CD2 C:HIS3282 3.1 36.8 1.0
OE1 C:GLU3316 3.1 37.5 1.0
CE1 C:HIS3282 3.2 35.1 1.0
CB C:ASP3342 3.4 39.4 1.0
CB C:CYS3076 3.5 37.9 1.0
NH2 C:ARG3107 3.8 46.5 1.0
CA C:CYS3076 4.0 36.9 1.0
OD1 C:ASP3342 4.1 38.8 1.0
ND1 C:HIS3282 4.2 37.7 1.0
CG C:HIS3282 4.3 38.0 1.0
CG C:GLU3316 4.3 38.2 1.0
NZ C:LYS3112 4.4 53.6 1.0
O C:HOH2053 4.5 35.9 1.0
O C:CYS3076 4.6 37.8 1.0
CA C:ASP3342 4.7 38.2 1.0
C C:CYS3076 4.7 36.5 1.0
CZ C:ARG3107 4.8 44.3 1.0
N C:ASP3342 4.8 37.2 1.0
CG C:LYS3112 4.9 52.7 1.0

Manganese binding site 4 out of 4 in 1ofq

Go back to Manganese Binding Sites List in 1ofq
Manganese binding site 4 out of 4 in the Crystal Structure of the Tyrosine-Regulated 3-Deoxy-D-Arabino- Heptulosonate-7-Phosphate Synthase From Saccharomyces Cerevisiae in Complex with Manganese(II)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Structure of the Tyrosine-Regulated 3-Deoxy-D-Arabino- Heptulosonate-7-Phosphate Synthase From Saccharomyces Cerevisiae in Complex with Manganese(II) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn4000

b:42.1
occ:1.00
 OD2 D:ASP4342 2.0 41.1 1.0
OE2 D:GLU4316 2.0 43.5 1.0
O D:HOH2002 2.1 40.4 1.0
NE2 D:HIS4282 2.3 33.5 1.0
SG D:CYS4076 2.5 40.3 1.0
CD D:GLU4316 3.0 43.8 1.0
CG D:ASP4342 3.0 40.4 1.0
CE1 D:HIS4282 3.2 35.0 1.0
CD2 D:HIS4282 3.3 35.4 1.0
OE1 D:GLU4316 3.3 43.3 1.0
CB D:ASP4342 3.5 40.9 1.0
O D:HOH2025 3.6 36.3 1.0
CB D:CYS4076 3.6 39.5 1.0
CA D:CYS4076 4.1 38.8 1.0
OD1 D:ASP4342 4.1 40.1 1.0
NH2 D:ARG4107 4.3 34.1 1.0
CG D:GLU4316 4.3 44.0 1.0
ND1 D:HIS4282 4.3 36.1 1.0
CG D:HIS4282 4.4 36.4 1.0
O D:HOH2071 4.5 28.1 1.0
O D:HOH2048 4.6 49.1 1.0
O D:CYS4076 4.7 39.3 1.0
C D:CYS4076 4.8 38.1 1.0
CA D:ASP4342 4.8 40.4 1.0
N D:ASP4342 4.9 39.5 1.0

Reference:

V.Koenig, A.Pfeil, G.H.Braus, T.R.Schneider. Substrate and Metal Complexes of 3-Deoxy-D-Arabino-Heptulosonate-7-Phosphate Synthase From Saccharomyces Cerevisiae Provide New Insights Into the Catalytic Mechanism J.Mol.Biol. V. 337 675 2004.
ISSN: ISSN 0022-2836
PubMed: 15019786
DOI: 10.1016/J.JMB.2004.01.055
Page generated: Sat Oct 5 11:56:10 2024

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